The presence of fetal DNA in maternal plasma has opened up exciting possibilities for noninvasive prenatal testing [1, 2]. Recently, there has been much interest in the use of massively parallel sequencing (MPS) for analyzing circulating fetal DNA for prenatal testing purposes. Thus, fetal trisomies 21, 13, 18 and selected sex chromosomal aneuploidies have been detected using MPS on maternal plasma DNA [3-7] and have been rapidly introduced into clinical service.
Apart from abnormalities due to copy number changes involving a whole chromosome, it would be important to evaluate whether the MPS-based analysis of maternal plasma might be sensitive enough for detecting subchromosomal deletions or duplications. In this regard, Peters et al reported the detection of a 4.2 Mb deletion on chromosome 12 in a maternal plasma sample obtained at the 35th week of gestation [8]. Jensen et al reported the detection of a 3 Mb deletion on chromosome 22 in maternal plasma samples obtained from two pregnant women at the 19th and 20th weeks of gestation [9]. Apart from the deleted region, Peters et al also performed statistical analysis on another region on chromosome 12, as well as 20 nonoverlapping 4 Mb regions on chromosome 14 [8]. Jensen et al, on the other hand, only focused their statistical analysis on the deleted region on chromosome 22 [9]. Thus, from the data presented by Peters et al and Jensen et al, it is not clear if the approach would be robust enough for a genomewide survey of microdeletions or microduplications, or indeed for the noninvasive determination of a fetal karyotype.
Lo et al reported that fetal single nucleotide polymorphisms (SNPs) can be genotyped in a genomewide scale using maternal plasma DNA sequencing [10]. In particular, these investigators have demonstrated that SNP alleles and mutations for single gene disorders that are inherited by a fetus from its mother can be elucidated by a process called relative haplotype dosage analysis [10]. Fan et al confirmed the robustness of relative haplotype dosage analysis and used this approach to detect a ˜2.85 Mb deletion inherited by a fetus from its mother [11]. There are two concerns for using this method for the clinical implementation of noninvasive prenatal karyotyping. First, this method requires maternal haplotyping to be performed which would require additional analytical steps [12, 13] or pedigree analysis. Second, it is unclear if this method could be used to detect de novo subchromosomal deletion or duplication.